The accurate analysis of molecular variation is important in a range of disciplines of parasitology. Although conventional DNA techniques have overcome some of the limitations of traditional approaches, some can be relatively expensive and/or cumbersome to use when large sample sizes require analysis, and some cannot accurately resolve or define nucleotide variation. Using selected examples of applications to parasites, Robin Gasser and Xingquan Zhu discuss some PCR-based mutation detection techniques and their advantages over conventional analytical methods.